Issues

• Crash if dna_reference not provided

  bug
  DessimozLab/read2tree#81 · Filter by author nromashchenko opened on Nov 14, 2025

• Can't process whitespaces in the read filenames

  Bug

  DessimozLab/read2tree#80 · Filter by author nromashchenko opened on Nov 12, 2025
  2

• reat2tree run seems to go well but species not added to the tree.

  DessimozLab/read2tree#79 · Filter by author mathildeparis opened on Oct 27, 2025
  4

• OMA

  DessimozLab/read2tree#68 · Filter by author cyxiang1027 opened on Jul 15, 2025
  2

• Question: generate marker genes from mitochondrion refseq

  DessimozLab/read2tree#67 · Filter by author brutal588 opened on Oct 15, 2024
  2

• TypeError: cannot unpack non-iterable NoneType object

  DessimozLab/read2tree#60 · Filter by author pengyan19 opened on Apr 17, 2024
  3

• AttributeError when running OGset.py

  DessimozLab/read2tree#59 · Filter by author scuadros28 opened on Mar 8, 2024
  11

• BUG?: KeyError(s) when running read2tree

  DessimozLab/read2tree#58 · Filter by author almosnow opened on Mar 6, 2024
  3

• QUESTION: Hetero sites.

  DessimozLab/read2tree#53 · Filter by author brgonzlez opened on Dec 11, 2023

• Adding species but not repeating the mapping of existing species

  enhancementquestion
  DessimozLab/read2tree#51 · Filter by author QuyANgo opened on Nov 29, 2023
  1

• IndexError: list assignment index out of range in Mapper.py

  DessimozLab/read2tree#46 · Filter by author bernard-kim opened on Oct 16, 2023
  1

• RuntimeError: generator raised StopIteration

  DessimozLab/read2tree#45 · Filter by author bernard-kim opened on Oct 16, 2023

• Error for some reads when conducting mapping step

  DessimozLab/read2tree#42 · Filter by author GYQ-form opened on Sep 10, 2023
  4

• possible error in the help message of --sample_reads

  documentation
  DessimozLab/read2tree#40 · Filter by author lilindu opened on Sep 3, 2023
  1

• OGs did not have any DNA

  DessimozLab/read2tree#36 · Filter by author Alfred-RRu opened on Aug 16, 2023
  4

• read2tree can't find corresponding CDS for each OMA group

  DessimozLab/read2tree#33 · Filter by author sci-study opened on Jul 12, 2023
  2

• How to add more marker genes

  DessimozLab/read2tree#28 · Filter by author brgonzlez opened on May 15, 2023
  10

• TypeError: __init__() takes 2 positional arguments but 3 were given

  DessimozLab/read2tree#24 · Filter by author marcejuarez90 opened on May 5, 2023
  3

• Error with ngm binary

  DessimozLab/read2tree#23 · Filter by author 3miumi opened on Apr 27, 2023
  4

• Can read2tree be run offline and with custom marker gene list?

  DessimozLab/read2tree#22 · Filter by author masudermann opened on Apr 26, 2023
  3

• Installation issue

  DessimozLab/read2tree#19 · Filter by author dhpalmer opened on Apr 21, 2023
  5

• No tree generated after running multiple species mode

  DessimozLab/read2tree#8 · Filter by author wrengs opened on Aug 26, 2022
  13